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inherit params from vis_clus
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R/vis_image.R

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#' This function visualizes the histology image for selected sample. Matches
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#' crop and settings of [vis_clus()] and [vis_gene()].
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#'
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#' @param spe A
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#' [SpatialExperiment-class][SpatialExperiment::SpatialExperiment-class]
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#' object. See [fetch_data()] for how to download some example objects or
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#' [read10xVisiumWrapper()] to read in `spaceranger --count` output files and
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#' build your own `spe` object.
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#' @param sampleid A `character(1)` specifying which sample to plot from
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#' `colData(spe)$sample_id` (formerly `colData(spe)$sample_name`).
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#' @param image_id A `character(1)` with the name of the image ID you want to
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#' use in the background.
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#' @param is_stitched A \code{logical(1)} vector: If `TRUE`, expects a
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#' [SpatialExperiment-class][SpatialExperiment::SpatialExperiment-class] built
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#' with `visiumStitched::build_spe()`.
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#' <http://research.libd.org/visiumStitched/reference/build_spe.html>; in
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#' particular, expects a logical colData column `exclude_overlapping`
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#' specifying which spots to exclude from the plot. Sets `auto_crop = FALSE`.
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#' @inheritParams vis_clus
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#' @param title_suffix A `character(1)` passed to [paste()][base::paste] to
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#' modify the title of the plot following the `sampleid`.
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#'

man/vis_image.Rd

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